How do you suppose that works out? Did he actually rule? Or was he just some uncontested 'God' doing whatever he pleased with the ponies of Equestria and they just took it? Did he 'rule' as himself or Pony form?
Well... here is one take of it...
Discord ruled in pony/alicorn form, which allowed him to set things up from the top down... to perpetuate his love of... discord. While he throws about random chaos stuff around Equestria between setting up his discord machinations.
Being the master of discord and possibly loving the challenge of it, he would set-up some strong pony personalities into leadership positions. Then he works to subtly subvert those personalities slowly. (Not as fast as he done with the mane 6, since he has tons of time here...)
As he subverts those personalities, he makes sure that their 'leadership' doesn't just crumble before it all starts... and if it does break down later, would be replaced later with another 'strong pony personality'.
Then, he sets em against each other, prodding them to bring more ponies into the mess and nudging along 'hateful' speech and sentiments among the ponies...
Equestria at war with herself, but not fallling apart from it. Pony hate/discord being widespread and what-not.
And he continues on in the small scale level of breaking up random friends and what-not, to sate his discord-ness between the lulls.
Physical
Perk: 5th Hoof
Description: You can use that glorified fanny duster of yours as if it was another limb, heck, its probably better, at least when you wanna work with the finer stuff unfit for hooves. An incredible feet, considering its just hair. Perhaps you shouldn't trim your tail...
Perk: Heavy Set
Description: Damn, you are big for a pony. A bit slower, but who needs speed when you got the strength and stamina to keep to keep on going?
Perk: Made of Something Else
Description: Ever moved so fast that it feels like you'd fall apart, painfully? No? Good, cause not everypony can even move that fast. But, some ponies can and fewer of those have the mettle to withstand that speed, you are one of them.
You are more resistant to pain, also allowing you to take much more of a beating before your body would give out right from under you.
Mental
Perk: Multi-Tasker
Description: Sure, some ponies are able to do a few simple things at the same time, but you, you can work on multiple complicated things at the same time, or at least do it much faster then normal. While lesser ponies need to put their full attention on that 1 thing.
Perk: Twitchy Sense
Description: You are capable of sensing imminint 'danger', for you and those you are with. They didn't listen, so who's laughing now? Oh, nopony is.
Perk: Wild Charm
Description: There is just something about you, something that nopony could explain, but animals love you... or something, who knows. Most of them anyways.
Animals of the wild are much less likely to attack you and your party. The more harmless critters are more likely to befriend you or at least come to bask in whatever it is about you, not your friends, just you.
For some odd reason, wild creatures who live in areas heavily frequented by ponies tend to... not want to be your friend. Why is that? Maybe if them damned tourists stopped feeding the wild animals.
Pegasi Uniques
Perk: Cloud Manipulation
Description: Walking on clouds, thats what you do. Heck, you can even sleep on em. Oh yea, you can freely move them around and could even disperse them if you smack em with your hooves.
Perk: Flight
Description: Hey, you! Yea, you! The one with the wings! You can fly!
Unicorn Magic
Type: Telekinesis
Description: The most basic of Unicorn magic. Pick up stuff, move stuff, just about any Unicorn can do it.
Type: Illusion
Description: The ability to make others see/touch/hear/taste/smell something you made up. Some ponies would swear up and down that what they experienced really happened.
Type: Energy
Description: Raw magic energy, unbridled, it can be used to hurt others, but, when properly manipulated, you can put up barriers and so much more.